As Salon explains in their retraction notice, the online magazine had co-published the piece with Rolling Stone. The notice reads, in part:

In the days after running “Deadly Immunity,” we amended the story with five corrections (which can still be found logged here) that went far in undermining Kennedy’s exposé. At the time, we felt that correcting the piece — and keeping it on the site, in the spirit of transparency — was the best way to operate. But subsequent critics, including most recently, Seth Mnookin in his book “The Panic Virus,” further eroded any faith we had in the story’s value. We’ve grown to believe the best reader service is to delete the piece entirely.

“I regret we didn’t move on this more quickly, as evidence continued to emerge debunking the vaccines and autism link,” says former Salon editor in chief Joan Walsh, now editor at large. “But continued revelations of the flaws and even fraud tainting the science behind the connection make taking down the story the right thing to do.” The story’s original URL now links to our autism topics page, which we believe now offers a strong record of clear thinking and skeptical coverage we’re proud of — including the critical pursuit of others who continue to propagate the debunked, and dangerous, autism-vaccine link.

Of note: Rolling Stone deleted the story from its site sometime last year, without notice or explanation. That link now has a 404 error. However, it has been archived at WebCitation.org.

As it happens, one of us (Ivan) is here in Research Triangle Park, North Carolina, for Science Online 2011, and so is Seth Mnookin, whose book Salon credited in their retraction. We asked Mnookin for his thoughts on it. (Full disclosure: Ivan and Seth are friends from college, and they’ll be talking about his book on a Reuters webcast on Tuesday, Jan. 18.)

He applauded Salon’s move, and contrasted it with Rolling Stone’s handling of criticism. In particular, he pointed Retraction Watch to a note Rolling Stone had attached to their version on July 14, 2005, about a month after it was first posted:

What is most striking is the lengths to which major media outlets have gone to disparage the story and to calm public fears — even in the face of the questionable science on the subject. In a segment on World News Tonight titled “A Closer Look,” ABC pointed out that Kennedy is “not a scientist or a doctor” and dismissed his extensive evidence as nothing more than “a few scientific studies.” The network also trotted out its medical editor, Dr. Timothy Johnson, to praise the “impeccably impartial Institute of Medicine” and to again state that Kennedy is not a scientist.

The New York Times, in a front-page story on the subject, devoted only one line to Kennedy’s article, which it said accused public-health officials and drugmakers of “conspiring” to hide the data on autism — a word that our story neither used nor implied. (The Wall Street Journal, in an op-ed attacking the article, was even more misleading, using the word “conspiracy” four times.) The Times then went on, for more than a full page, to portray concerns over vaccines as nothing more than the misguided fears of parents who suffer from “scientific illiteracy,” unable to understand the medical studies that prove immunizations to be safe. It depicted studies reviewed by the Institute of Medicine as definitive without even bothering to address the host of serious questions raised about their validity: conflicting diagnoses of autism, mixed-up data from HMOs and research skewed to exclude many sick kids.

….

It is important to note, however, that none of the mistakes weaken the primary point of the story. The government’s own records show that it has failed to do the science necessary to put to rest reasonable concerns about vaccines. If the scientists had simply done their job rather than covering their tracks, there would be no controversy today. Instead, the government cannot even provide a definitive figure of the number of cases of autism among American children — a number obviously critical to any serious scientific investigation — and yet expects the public to believe that it has ruled out any link between vaccines and an illness it does not even track.

“Science,” as one doctor in our story insisted, “is best left to scientists.” But when the scientists fail to do their job, resorting to closed-door meetings and rigged studies, others in society have not only a right but a moral obligation to question their work. In the coming years, further research may indeed demonstrate that mercury in vaccines is not responsible for the rise in autism. For now, though, we can only raise a very real and legitimate alarm — and hope that the government’s well-documented mishandling of its own research did not needlessly jeopardize the health of hundreds of thousands of children.

Mnookin tells Retraction Watch:

Salon didn’t do something like that. They printed the corrections, and didn’t start getting aggressive about the fact that 500 words of corrections made no difference in the underlying accuracy of the story.

Mnookin’s book, The Panic Virus, includes a whole chapter about piece. He went on:

There are so many problems with the story. It shows what can be done with the fig leaf of fact-checking. You can make a statement that is technically correct and fundamentally wrong. That’s what happened here. He was taking quotes ridiculously out of context. There was a transcript of hundreds of pages. The piece took quotes that were dozens of pages apart and connected them with an ellipsis.

What struck Mnookin was Rolling Stone’s refusal to admit error:

People make mistakes. It’s just a reality of life. This was with the perspective of five years of hindsight and fact-checking. I was just surprised that they would dig in their feet in ways that seemed self-defeating.

Mnookin, for his part, has included a corrections page on his website for all three of his books. Here, for example, is the one for his first book, Hard News: The Scandals at the New York Times and Their Meaning for American Media. Of his new book, he said:

It’s a 110,000-word book. *It’s ridiculous to assume there aren’t going to be things that aren’t accurate. When I first [did the corrections pages, other journalists] were shocked. It’s such a fundamental misunderstanding of your audience. If there are things I got wrong, and people have pointed that out, why wouldn’t I want to correct that?

We agree wholeheartedly, of course, and wish that more scientific journals would adopt something similar. We also applaud Salon’s retraction and explanation.

Mnookin was quick to point out that he didn’t talk to Rolling Stone, and doesn’t know their internal process for dealing with the criticism. He tried to talk to Robert F. Kennedy Jr. before he published the book, but Kennedy didn’t agree to an interview.

Today’s retraction is important, as is any retraction, for correcting the record. It’s hard to know just how influential the piece was; there’s nothing for journalism exactly like citations that would at least give a sense of that. Still, says Mnookin:

Because of the nature of this story, I don’t think this piece was a touchstone that people kept coming back to that was driving the debate. One, thimerosal has been gone from vaccines for years, and two, more players kept coming on the scene. It hadn’t been held up as evidence. It was not one of those things.

Of note: The original uncorrected version of the piece is still posted at Kennedy’s site. We spot-checked the errors that Salon had corrected, and they’re still there.

Update, 7:20 a.m. Eastern, 1/18/11: In sentence marked with an asterisk, “are” changed to “aren’t” as “are” was a typo. Apologies for the error, and thanks to two commenters below for spotting it.

Good question about timing. I don’t know of any study of media outlet retractions like this, but in a recent post we wrote about a study that found journal retractions taking place years after the original studies were published — in one case nine years.

Without being a conspiracy theorist, I have wondered if the vaccine scare was funded by firms that have a vested interest in preventing epidemiological or clinical evidence from emerging about their products, like pesticide makers. Cigarette companies certainly spent decades funding groups to try to push the blame elsewhere, and continue to use money to sell story that cigarettes aren’t a significant contributor to cancer and lung disease.

The realist in me says, though, that the millions of synthetic chemicals to which we are exposed constantly in food, water, and air in unexpected and untested combinations likely are part of the root of all kinds of health issues.

(There’s also an argument to be made that autism hasn’t been on the rise. That better diagnostic tools and testing, and better mainstream acceptance of autism as part of life, has led to a far greater diagnosis. There’s no apples-to-apples comparison with 2011 diagnosis versus, say, 1996.)

The BMJ indicated that they would review papers by Wakefield that are in their journals. This includes the Uhlman paper in which Mr. Wakefield’s team claimed to find vaccine strain measles virus RNA in tissue samples.

The PCR methods were shown to be poor by Stephen Bustin. Mr. Wakefield was shown to have ignored negative test results from his own lab in the Royal Free. Avreplication attempt was negative. The patient pool had some of the lancet kids, if not all, plus other kids with the same biased referall history. Mr. Wakefield had a conflict of interest in multiple undeclared ways.